The decoding of human genome is now progressing and helping clarify causal relations between various diseases or diatheses and specific gene sequences. For example, such a gene analysis is intended to use for predicting the onset of diseases, side effects of drugs, etc.
A means conventionally used for gene analysis is gel-based electrophoresis. In recent years, capillary gel electrophoresis has been developed with the aim of separating and analyzing trace amounts of biological samples in a short time. Capillary gel electrophoresis uses glass capillaries filled with a hydrogel such as acrylamide.
In addition, microarrays carrying multiple capture probes for DNA or protein detection (i.e., probes capable of capturing target DNA or protein molecules and the like through hybridization or binding to the DNA or protein molecules to be detected) are employed as useful tools for detecting mutations and expression levels of many genes all at once. Such microarrays are also known to have a large number of variations which are constructed using a gel. Among them, microarrays known to use a gel for immobilization of capture probes include, for example, those having multiple slots or holes on a substrate (e.g., a resin board), in which the slots or holes are filled with a DNA-containing gel (see JP 2000-60554 A), as well as those having gel spots containing DNA or other substances on a flat substrate (see U.S. Pat. No. 5,770,721). Also, some of the inventors of the present invention have developed a microarray that is obtained by creating a hollow fiber alignment comprising hollow fibers whose hollow space is filled with a capture probe-containing gel and then cutting the alignment in a direction intersecting with its fiber axis. This microarray has been filed for patent application (see JP 2000-270877 A, JP 2000-270878 A and JP 2000-270879 A).
These capture probe-immobilized microarrays may be used for hybridization with an analyte to detect specific nucleotide sequences. Detection of hybrids is accomplished by using a known means capable of specifically recognizing the hybrids, as exemplified by fluorescence detection.
However, there has been a problem that when the microarrays after hybridization are measured for fluorescence intensity in each of their compartments where capture probes are immobilized, the fluorescence intensity is higher in the outer regions of the compartments, but lower in the center regions of the compartments.